[Ifeffit] Problems with fit in pyrite structure with Se substitution

[Adriana Matamoros Veloza]

Hi Bruce, Matt,

Fantastic!  Many thanks for your help, I will try that and will let you know.

Best wishes,

Adriana :)



-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel
Sent: 03 July 2012 13:55
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Problems with fit in pyrite structure with Se substitution

On Tuesday, July 03, 2012 09:26:38 AM Adriana Matamoros Veloza wrote:
> In both projects the data corresponds to Se edge (no sulphur).  Selenium
> data was collected on natural pyrite grains.  When Se associates to pyrite,
> it is normally inferred that Se substituted sulphur within the pyrite
> structure.  Both elements are chemically very similar. Looking at selenium
> as the core atom, we want to see if it is possible to get the chemical
> environment related to pyrite (Se-S, Se-Fe bonds).  In natural environments
> if substitution of sulphur with selenium occurs the proportion is rather
> than low (perhaps maximum 1% of the population of sulphur atoms). So, in
> that case we are expecting to get data that fit to the pyrite structure
> taking Se as the core atom.  For that reason, the Feff calculations were
> made with the crystal structure of pyrite with sulphur as the core atom and
> used Se edge instead.  Is that making any sense?

I understand what you are trying to do, but what you actually did
isn't very sensible.

If Se is the central atom in the experiment, Se must be the central
atom in the Feff calculation.  The central atom phase shift (see
http://leonardo.phys.washington.edu/feff/wiki/index.php?title=FEFF_Variables)
for Se is very different from S.  If you get that so wrong, it will
have a profound impact on the evaluation of E0 and DeltaR.

Here's a snippet from the feff input that you used:

  POTENTIALS
  * ipot   Z      tag
     0     16     S         
     1     26     Fe        
     2     16     S         


 ATOMS                  * this list contains 170 atoms
 *   x          y          z     ipot tag           distance
    0.00000    0.00000    0.00000  0  S1            0.00000
    1.25695    1.25695    1.25695  2  S1.1          2.17711
   -2.08047    0.62848    0.62848  1  Fe1.1         2.26237
    0.62848   -2.08047    0.62848  1  Fe1.1         2.26237
    0.62848    0.62848   -2.08047  1  Fe1.1         2.26237

It needs to be edited to read

  POTENTIALS
  * ipot   Z      tag
     0     34     Se
     1     26     Fe        
     2     16     S         


 ATOMS                  * this list contains 170 atoms
 *   x          y          z     ipot tag           distance
    0.00000    0.00000    0.00000  0  Se            0.00000
    1.25695    1.25695    1.25695  2  S1.1          2.17711
   -2.08047    0.62848    0.62848  1  Fe1.1         2.26237
    0.62848   -2.08047    0.62848  1  Fe1.1         2.26237
    0.62848    0.62848   -2.08047  1  Fe1.1         2.26237

The truly important change was to change the Z for potential 0 from 16
to 34.  That tells Feff that the central atom is Se.  The other two
edits help Artemis help you understand the calculation.

This illustrates an aspect of how Artemis works.  In principle, it
should not be necessary to press the "Run Atoms" button then to press
the "Run Feff" button in order to make a Feff calculation happen.  In
many situation, those two buttons are pushed in quick succession,
making the second button press seemingly unnecessary.

There are, however, many analysis situations where it is useful for
the user to pause between the two button presses and ponder feff's
input data.  In this case, you need to change the absorber to deal
with the situation of having measured XAS at the edge of the dopant.

Try that.  I suspect your analysis will make more sense.

B

-- 

 Bruce Ravel  ------------------------------------ bravel at bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 Homepage:    http://xafs.org/BruceRavel
 Software:    https://github.com/bruceravel
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